A protein A-colloidal gold immunoelectron microscopy (PAG-IEM) technique was developed for the detection of bovine coronavirus (BCV) in the feces and nasal secretions of infected calves. Feces or nasal swab fluids were incubated sequentially with hyperimmune bovine anti-bovine coronavirus serum and protein A-gold, negatively stained, applied to formvar-coated copper grids and viewed using an electron microscope. The PAG-IEM method specifically identified BCV particles and possible subviral particles in feces and nasal-swab fluids from infected calves. The PAG-IEM method did not label other enveloped enteric viruses or morphologically similar fringed particles commonly found in feces. Detection of BCV using PAG-IEM was compared with ELISA and direct immunofluorescence (IF) of nasal epithelial cells by monitoring fecal and respiratory tract shedding of BCV from two experimentally infected and two naturally infected calves from birth to 3 weeks of age. PAG-IEM and ELISA detected shedding of BCV in fecal (4/4 animals) and nasal (3/4 animals) samples for an average of 5.25 days each. The observed agreement of BCV detection by PAG-IEM and ELISA was 85%. PAG-IEM may be a more sensitive immunoassay for the detection of BCV in diagnostic specimens from infected neonatal calves than ELISA. BCV infection of nasal epithelial cells was detected by immunofluorescence in 4/4 calves, persisted for the duration of the study in 2/4 calves and was sporadic in the other two animals. The observed agreement of BCV detection by PAG-IEM and IF was 57%.